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Joint species distribution models (JSDM) are among the most important statistical tools in community ecology. They are routinely used for inference and various prediction tasks, such as to build species distribution maps or biomass estimation over spatial areas. Existing JSDM's cannot, however, model mutual exclusion between species, which may happen in some species groups, such as mosses in the bottom layer of a peatland site. We tackle this deficiency in the context of modeling plant percentage cover data, where mutual exclusion arises from limited growing space and competition for light. We propose a hierarchical JSDM where multivariate latent Gaussian variable model describes species' niche preferences and Dirichlet-Multinomial distribution models the observation process and exclusive competition for space between species. We use both stationary and non-stationary multivariate Gaussian processes to model residual phenomena. We also propose a decision theoretic model comparison and validation approach to assess the goodness of JSDMs in four different types of predictive tasks. We apply our models and methods to a case study on modeling vegetation cover in a boreal peatland. Our results show that ignoring the interspecific interactions and competition for space significantly reduces models' predictive performance and leads to biased estimates for total percentage cover both for individual species and over all species combined. A model's relative predictive performance also depends on the model comparison methods highlighting that model comparison and assessment should resemble the true predictive task. Our results also demonstrate that the proposed joint species distribution model can be used to simultaneously infer interspecific correlations in niche preference as well as mutual exclusive competition for space and through that provide novel insight into ecological research.

While the empirical success of self-supervised learning (SSL) heavily relies on the usage of deep nonlinear models, existing theoretical works on SSL understanding still focus on linear ones. In this paper, we study the role of nonlinearity in the training dynamics of contrastive learning (CL) on one and two-layer nonlinear networks with homogeneous activation $h(x) = h'(x)x$. We have two major theoretical discoveries. First, the presence of nonlinearity can lead to many local optima even in 1-layer setting, each corresponding to certain patterns from the data distribution, while with linear activation, only one major pattern can be learned. This suggests that models with lots of parameters can be regarded as a \emph{brute-force} way to find these local optima induced by nonlinearity. Second, in the 2-layer case, linear activation is proven not capable of learning specialized weights into diverse patterns, demonstrating the importance of nonlinearity. In addition, for 2-layer setting, we also discover \emph{global modulation}: those local patterns discriminative from the perspective of global-level patterns are prioritized to learn, further characterizing the learning process. Simulation verifies our theoretical findings.

In the semi-supervised setting where labeled data are largely limited, it remains to be a big challenge for message passing based graph neural networks (GNNs) to learn feature representations for the nodes with the same class label that is distributed discontinuously over the graph. To resolve the discontinuous information transmission problem, we propose a control principle to supervise representation learning by leveraging the prototypes (i.e., class centers) of labeled data. Treating graph learning as a discrete dynamic process and the prototypes of labeled data as "desired" class representations, we borrow the pinning control idea from automatic control theory to design learning feedback controllers for the feature learning process, attempting to minimize the differences between message passing derived features and the class prototypes in every round so as to generate class-relevant features. Specifically, we equip every node with an optimal controller in each round through learning the matching relationships between nodes and the class prototypes, enabling nodes to rectify the aggregated information from incompatible neighbors in a graph with strong heterophily. Our experiments demonstrate that the proposed PCGCN model achieves better performances than deep GNNs and other competitive heterophily-oriented methods, especially when the graph has very few labels and strong heterophily.

Robustness and resilience of simultaneous localization and mapping (SLAM) are critical requirements for modern autonomous robotic systems. One of the essential steps to achieve robustness and resilience is the ability of SLAM to have an integrity measure for its localization estimates, and thus, have internal fault tolerance mechanisms to deal with performance degradation. In this work, we introduce a novel method for predicting SLAM localization error based on the characterization of raw sensor inputs. The proposed method relies on using a random forest regression model trained on 1-D global pooled features that are generated from characterized raw sensor data. The model is validated by using it to predict the performance of ORB-SLAM3 on three different datasets running on four different operating modes, resulting in an average prediction accuracy of up to 94.7\%. The paper also studies the impact of 12 different 1-D global pooling functions on regression quality, and the superiority of 1-D global averaging is quantitatively proven. Finally, the paper studies the quality of prediction with limited training data, and proves that we are able to maintain proper prediction quality when only 20 \% of the training examples are used for training, which highlights how the proposed model can optimize the evaluation footprint of SLAM systems.

We study the spectral convergence of a symmetrized Graph Laplacian matrix induced by a Gaussian kernel evaluated on pairs of embedded data, sampled from a manifold with boundary, a sub-manifold of $\mathbb{R}^m$. Specifically, we deduce the convergence rates for eigenpairs of the discrete Graph-Laplacian matrix to the eigensolutions of the Laplace-Beltrami operator that are well-defined on manifolds with boundary, including the homogeneous Neumann and Dirichlet boundary conditions. For the Dirichlet problem, we deduce the convergence of the \emph{truncated Graph Laplacian}, which is recently numerically observed in applications, and provide a detailed numerical investigation on simple manifolds. Our method of proof relies on the min-max argument over a compact and symmetric integral operator, leveraging the RKHS theory for spectral convergence of integral operator and a recent pointwise asymptotic result of a Gaussian kernel integral operator on manifolds with boundary.

Oversmoothing is a central challenge of building more powerful Graph Neural Networks (GNNs). While previous works have only demonstrated that oversmoothing is inevitable when the number of graph convolutions tends to infinity, in this paper, we precisely characterize the mechanism behind the phenomenon via a non-asymptotic analysis. Specifically, we distinguish between two different effects when applying graph convolutions -- an undesirable mixing effect that homogenizes node representations in different classes, and a desirable denoising effect that homogenizes node representations in the same class. By quantifying these two effects on random graphs sampled from the Contextual Stochastic Block Model (CSBM), we show that oversmoothing happens once the mixing effect starts to dominate the denoising effect, and the number of layers required for this transition is $O(\log N/\log (\log N))$ for sufficiently dense graphs with $N$ nodes. We also extend our analysis to study the effects of Personalized PageRank (PPR), or equivalently, the effects of initial residual connections on oversmoothing. Our results suggest that while PPR mitigates oversmoothing at deeper layers, PPR-based architectures still achieve their best performance at a shallow depth and are outperformed by the graph convolution approach on certain graphs. Finally, we support our theoretical results with numerical experiments, which further suggest that the oversmoothing phenomenon observed in practice can be magnified by the difficulty of optimizing deep GNN models.

Knowledge graph embedding (KGE) is a increasingly popular technique that aims to represent entities and relations of knowledge graphs into low-dimensional semantic spaces for a wide spectrum of applications such as link prediction, knowledge reasoning and knowledge completion. In this paper, we provide a systematic review of existing KGE techniques based on representation spaces. Particularly, we build a fine-grained classification to categorise the models based on three mathematical perspectives of the representation spaces: (1) Algebraic perspective, (2) Geometric perspective, and (3) Analytical perspective. We introduce the rigorous definitions of fundamental mathematical spaces before diving into KGE models and their mathematical properties. We further discuss different KGE methods over the three categories, as well as summarise how spatial advantages work over different embedding needs. By collating the experimental results from downstream tasks, we also explore the advantages of mathematical space in different scenarios and the reasons behind them. We further state some promising research directions from a representation space perspective, with which we hope to inspire researchers to design their KGE models as well as their related applications with more consideration of their mathematical space properties.

Graph neural networks generalize conventional neural networks to graph-structured data and have received widespread attention due to their impressive representation ability. In spite of the remarkable achievements, the performance of Euclidean models in graph-related learning is still bounded and limited by the representation ability of Euclidean geometry, especially for datasets with highly non-Euclidean latent anatomy. Recently, hyperbolic space has gained increasing popularity in processing graph data with tree-like structure and power-law distribution, owing to its exponential growth property. In this survey, we comprehensively revisit the technical details of the current hyperbolic graph neural networks, unifying them into a general framework and summarizing the variants of each component. More importantly, we present various HGNN-related applications. Last, we also identify several challenges, which potentially serve as guidelines for further flourishing the achievements of graph learning in hyperbolic spaces.

The area of Data Analytics on graphs promises a paradigm shift as we approach information processing of classes of data, which are typically acquired on irregular but structured domains (social networks, various ad-hoc sensor networks). Yet, despite its long history, current approaches mostly focus on the optimization of graphs themselves, rather than on directly inferring learning strategies, such as detection, estimation, statistical and probabilistic inference, clustering and separation from signals and data acquired on graphs. To fill this void, we first revisit graph topologies from a Data Analytics point of view, and establish a taxonomy of graph networks through a linear algebraic formalism of graph topology (vertices, connections, directivity). This serves as a basis for spectral analysis of graphs, whereby the eigenvalues and eigenvectors of graph Laplacian and adjacency matrices are shown to convey physical meaning related to both graph topology and higher-order graph properties, such as cuts, walks, paths, and neighborhoods. Next, to illustrate estimation strategies performed on graph signals, spectral analysis of graphs is introduced through eigenanalysis of mathematical descriptors of graphs and in a generic way. Finally, a framework for vertex clustering and graph segmentation is established based on graph spectral representation (eigenanalysis) which illustrates the power of graphs in various data association tasks. The supporting examples demonstrate the promise of Graph Data Analytics in modeling structural and functional/semantic inferences. At the same time, Part I serves as a basis for Part II and Part III which deal with theory, methods and applications of processing Data on Graphs and Graph Topology Learning from data.

In many real-world network datasets such as co-authorship, co-citation, email communication, etc., relationships are complex and go beyond pairwise. Hypergraphs provide a flexible and natural modeling tool to model such complex relationships. The obvious existence of such complex relationships in many real-world networks naturaly motivates the problem of learning with hypergraphs. A popular learning paradigm is hypergraph-based semi-supervised learning (SSL) where the goal is to assign labels to initially unlabeled vertices in a hypergraph. Motivated by the fact that a graph convolutional network (GCN) has been effective for graph-based SSL, we propose HyperGCN, a novel GCN for SSL on attributed hypergraphs. Additionally, we show how HyperGCN can be used as a learning-based approach for combinatorial optimisation on NP-hard hypergraph problems. We demonstrate HyperGCN's effectiveness through detailed experimentation on real-world hypergraphs.